Raspberry Pi 3 + PiGrrl custom install; Controls don't seem to work correctly in RetroPie

[jlowe64]

Pi Model: Raspberry Pi 3 B
RetroPie Version Used: 4 beta
Built From: SD Image from retropie.org.uk, then upgraded via the setup script
USB Devices connected: 16 gig Sandisk drive
Controller used: Adafruit PiGrrl custom controller
Error messages received: none
Guide used: https://learn.adafruit.com/running-opengl-based-games-and-emulators-on-adafruit-pitft-displays/overview + https://learn.adafruit.com/pigrrl-2/overview
File: /opt/retropie/configs/all/retroarch.cfg ??
Emulator: all
Attachment of config files:
http://pastebin.com/rVHCZsvz

I used your official image successfully, then upgrade to the beta, because I was thinking that the new control files from Adafruit's controller (it simply emulates a new keyboard and has it load on boot) needed the newest version of RetroPie. When doing this, I realized it wasn't working. I've tested that it is not a hardware issue because I've used two different boards and they have the exact same issue between the two of them. I know it has to be software, perhaps communication between EmulationStation and RetroPie?

To give more details, on both boards from Adafruit my left pad is the a button, up is the b button, left bumper is left, right bumper is down. This only happens in RetroPie.

When I launch a rom, the controls mostly seem okay, although I think my retroarch.cfg file may have a bad key or two. That's definitely a config issue there, and please let me know if there's something glaring I should fix.

Any help is appreciated.